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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $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' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ), 'gf_id' => 'HOM05D001219', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001219' ), 'data_identifier' => 'HOM05D001219', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001219', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '513', 'num_species' => '75' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p45070' => 'bna', 'Aa31LG4G910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1324' => 'aag', 'Actinidia25444' => 'ach', 'Actinidia38319' => 'ach', 'Ah.11g044240' => 'amhyb', 'AL2G40810' => 'aly', 'arahy.Tifrunner.gnm1.ann1.158PZX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1BHQ1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2CLR18' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2F3432' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2MWS0I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6H8B8Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PP8TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6HDT7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G4PD56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GPF1Q4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J2ILTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JW8Z9M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR23UA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2NKR4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QYVZ3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S9WJEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7YMEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VNVE4D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9YH2' => 'arhy', 'AT1G80630' => 'ath', 'ATR0629G134' => 'atr', 'Atru.chr10.2383' => 'acertr', 'AUR62007700' => 'cqu', 'AUR62011476' => 'cqu', 'AUR62011477' => 'cqu', 'AUR62011478' => 'cqu', 'AUR62011479' => 'cqu', 'AUR62011481' => 'cqu', 'AUR62011485' => 'cqu', 'AUR62011661' => 'cqu', 'AUR62011662' => 'cqu', 'AUR62013441' => 'cqu', 'AUR62016288' => 'cqu', 'AUR62016289' => 'cqu', 'AUR62016290' => 'cqu', 'AUR62016291' => 'cqu', 'AUR62016292' => 'cqu', 'AUR62016293' => 'cqu', 'AUR62016295' => 'cqu', 'AUR62016323' => 'cqu', 'AUR62016484' => 'cqu', 'AUR62016485' => 'cqu', 'AUR62040408' => 'cqu', 'AUR62040410' => 'cqu', 'BolC6t40404H' => 'bol', 'BraA07t32010Z' => 'bra', 'C06p53900' => 'bna', 'CAN.G407.40' => 'can', 'CAN.G407.41' => 'can', 'CANSAT56G1867' => 'cansat', 'CARHR073890' => 'chi', 'Carub.0002s2711' => 'cru', 'Ca_04901_v3' => 'car', 'Ca_06859_v3' => 'car', 'Ca_07189_v3' => 'car', 'Ca_20555_v3' => 'car', 'Ca_20557_v3' => 'car', 'Ca_28544_v3' => 'car', 'Ca_30909_v3' => 'car', 'Ca_30910_v3' => 'car', 'CDE04G3743' => 'cde', 'Cfa001905' => 'cfa', 'Ciclev10027319m.g' => 'ccl', 'CiPaw.01G252300' => 'cil', 'ClCG09G003210' => 'cla', 'COL.COLO4_03340' => 'col', 'COL.COLO4_03373' => 'col', 'COL.COLO4_05684' => 'col', 'COL.COLO4_07203' => 'col', 'COL.COLO4_07221' => 'col', 'COL.COLO4_08738' => 'col', 'COL.COLO4_09972' => 'col', 'COL.COLO4_20760' => 'col', 'COL.COLO4_20761' => 'col', 'COL.COLO4_22355' => 'col', 'COL.COLO4_26644' => 'col', 'COL.COLO4_31198' => 'col', 'COL.COLO4_31329' => 'col', 'COL.COLO4_31467' => 'col', 'COL.COLO4_31649' => 'col', 'COL.COLO4_35451' => 'col', 'COL.COLO4_35901' => 'col', 'Cpa.g.sc10.120' => 'cpa', 'CsaV3_7G032020' => 'csa', 'CSS0005671' => 'camsi', 'CSS0017048' => 'camsi', 'CSS0020314' => 'camsi', 'CSS0032623' => 'camsi', 'CSS0037391' => 'camsi', 'CSS0049276' => 'camsi', 'DCAR_016287' => 'dca', 'DCAR_016288' => 'dca', 'DCAR_016289' => 'dca', 'Dinv23311' => 'din', 'Duzib106G0099' => 'dzi', 'Duzib106G0373' => 'dzi', 'Duzib106G0874' => 'dzi', 'Duzib106G1928' => 'dzi', 'Duzib160G0295' => 'dzi', 'Duzib235G0909' => 'dzi', 'ECA232G1154' => 'eca', 'EL10Ac7g16765' => 'bvu', 'EL10Ac8g20424' => 'bvu', 'Eucgr.E01273' => 'egr', 'Eucgr.E01286' => 'egr', 'Eucgr.F03944' => 'egr', 'FAN02G1796' => 'fan', 'FAN05G1445' => 'fan', 'FAN05G4962' => 'fan', 'FAN09G4190' => 'fan', 'FAN14G5953' => 'fan', 'FvH4_6g28940' => 'fve', 'FvH4_6g28950' => 'fve', 'Glyma.07G026100' => 'gma', 'Glyma.07G026200' => 'gma', 'Glyma.08G216300' => 'gma', 'Gohir.A05G121100' => 'ghi', 'Gohir.D05G122100' => 'ghi', 'Gorai.009G125600' => 'gra', 'HanXRQChr16g0500041' => 'han', 'Haze_16652' => 'cav', 'Hma1.2p1_0000F.1_g000390' => 'hma', 'Hma1.2p1_0135F.1_g061780' => 'hma', 'Lalb_Chr01g0011821' => 'lal', 'Lalb_Chr01g0011831' => 'lal', 'Lalb_Chr01g0012921' => 'lal', 'Lalb_Chr18g0057661' => 'lal', 'Lalb_Chr25g0279061' => 'lal', 'Lalb_Chr25g0279201' => 'lal', 'Lalb_Chr25g0279211' => 'lal', 'Lalb_Chr25g0279221' => 'lal', 'Lalb_Chr25g0279231' => 'lal', 'Lj3g0011098' => 'lja', 'Lj3g0020556' => 'lja', 'Lj3g0021238' => 'lja', 'Lj3g0021602' => 'lja', 'Lj9P496T46' => 'lonja', 'Lsat_1_v5_gn_4_86000' => 'lsa', 'Manes.04G105600' => 'mes', 'MBI15_g17828_MAGBIO' => 'mbi', 'Medtr0041s0060' => 'mtr', 'Medtr0105s0110' => 'mtr', 'Medtr0295s0010' => 'mtr', 'Medtr0345s0020' => 'mtr', 'Medtr0807s0010' => 'mtr', 'Medtr1155s0010' => 'mtr', 'Medtr1g023530' => 'mtr', 'Medtr1g028400' => 'mtr', 'Medtr1g028410' => 'mtr', 'Medtr1g042340' => 'mtr', 'Medtr1g050478' => 'mtr', 'Medtr1g069090' => 'mtr', 'Medtr1g069120' => 'mtr', 'Medtr1g069145' => 'mtr', 'Medtr1g075040' => 'mtr', 'Medtr1g115380' => 'mtr', 'Medtr1g115390' => 'mtr', 'Medtr2g007590' => 'mtr', 'Medtr2g078550' => 'mtr', 'Medtr2g103530' => 'mtr', 'Medtr2g104970' => 'mtr', 'Medtr3g006050' => 'mtr', 'Medtr3g008790' => 'mtr', 'Medtr3g036270' => 'mtr', 'Medtr3g073390' => 'mtr', 'Medtr3g074000' => 'mtr', 'Medtr3g074550' => 'mtr', 'Medtr3g074570' => 'mtr', 'Medtr3g081260' => 'mtr', 'Medtr3g081430' => 'mtr', 'Medtr3g083280' => 'mtr', 'Medtr3g110148' => 'mtr', 'Medtr3g110150' => 'mtr', 'Medtr3g110740' => 'mtr', 'Medtr3g465770' => 'mtr', 'Medtr4g005810' => 'mtr', 'Medtr4g006210' => 'mtr', 'Medtr4g006240' => 'mtr', 'Medtr4g006250' => 'mtr', 'Medtr4g006280' => 'mtr', 'Medtr4g006290' => 'mtr', 'Medtr4g006450' => 'mtr', 'Medtr4g006460' => 'mtr', 'Medtr4g006510' => 'mtr', 'Medtr4g006520' => 'mtr', 'Medtr4g008290' => 'mtr', 'Medtr4g008330' => 'mtr', 'Medtr4g008340' => 'mtr', 'Medtr4g008380' => 'mtr', 'Medtr4g008400' => 'mtr', 'Medtr4g008420' => 'mtr', 'Medtr4g008430' => 'mtr', 'Medtr4g008440' => 'mtr', 'Medtr4g008450' => 'mtr', 'Medtr4g008470' => 'mtr', 'Medtr4g008480' => 'mtr', 'Medtr4g008490' => 'mtr', 'Medtr4g008600' => 'mtr', 'Medtr4g009010' => 'mtr', 'Medtr4g009030' => 'mtr', 'Medtr4g009055' => 'mtr', 'Medtr4g010410' => 'mtr', 'Medtr4g010420' => 'mtr', 'Medtr4g010450' => 'mtr', 'Medtr4g010460' => 'mtr', 'Medtr4g010510' => 'mtr', 'Medtr4g010580' => 'mtr', 'Medtr4g010590' => 'mtr', 'Medtr4g010615' => 'mtr', 'Medtr4g010630' => 'mtr', 'Medtr4g010710' => 'mtr', 'Medtr4g010750' => 'mtr', 'Medtr4g010760' => 'mtr', 'Medtr4g010770' => 'mtr', 'Medtr4g010880' => 'mtr', 'Medtr4g010920' => 'mtr', 'Medtr4g010970' => 'mtr', 'Medtr4g011120' => 'mtr', 'Medtr4g011130' => 'mtr', 'Medtr4g012820' => 'mtr', 'Medtr4g016660' => 'mtr', 'Medtr4g016667' => 'mtr', 'Medtr4g019320' => 'mtr', 'Medtr4g021765' => 'mtr', 'Medtr4g021835' => 'mtr', 'Medtr4g024200' => 'mtr', 'Medtr4g024220' => 'mtr', 'Medtr4g035280' => 'mtr', 'Medtr4g035290' => 'mtr', 'Medtr4g059340' => 'mtr', 'Medtr4g129140' => 'mtr', 'Medtr4g132730' => 'mtr', 'Medtr4g133640' => 'mtr', 'Medtr4g435328' => 'mtr', 'Medtr4g435338' => 'mtr', 'Medtr5g039080' => 'mtr', 'Medtr5g039090' => 'mtr', 'Medtr5g046730' => 'mtr', 'Medtr5g067480' => 'mtr', 'Medtr5g067490' => 'mtr', 'Medtr5g067860' => 'mtr', 'Medtr5g067910' => 'mtr', 'Medtr5g068550' => 'mtr', 'Medtr5g075860' => 'mtr', 'Medtr5g087540' => 'mtr', 'Medtr5g088250' => 'mtr', 'Medtr5g095790' => 'mtr', 'Medtr5g095810' => 'mtr', 'Medtr5g095830' => 'mtr', 'Medtr5g430490' => 'mtr', 'Medtr6g016685' => 'mtr', 'Medtr6g016705' => 'mtr', 'Medtr6g016720' => 'mtr', 'Medtr6g016725' => 'mtr', 'Medtr6g016740' => 'mtr', 'Medtr6g016750' => 'mtr', 'Medtr6g016760' => 'mtr', 'Medtr6g016765' => 'mtr', 'Medtr6g016900' => 'mtr', 'Medtr6g016905' => 'mtr', 'Medtr6g016910' => 'mtr', 'Medtr6g016915' => 'mtr', 'Medtr6g018580' => 'mtr', 'Medtr6g022820' => 'mtr', 'Medtr6g025290' => 'mtr', 'Medtr6g027420' => 'mtr', 'Medtr6g033270' => 'mtr', 'Medtr6g034765' => 'mtr', 'Medtr6g042880' => 'mtr', 'Medtr6g042905' => 'mtr', 'Medtr6g054950' => 'mtr', 'Medtr6g080560' => 'mtr', 'Medtr7g024310' => 'mtr', 'Medtr7g029070' => 'mtr', 'Medtr7g029075' => 'mtr', 'Medtr7g029085' => 'mtr', 'Medtr7g029535' => 'mtr', 'Medtr7g044870' => 'mtr', 'Medtr7g100890' => 'mtr', 'Medtr8g017160' => 'mtr', 'Medtr8g037780' => 'mtr', 'Medtr8g045150' => 'mtr', 'Medtr8g045170' => 'mtr', 'Medtr8g045190' => 'mtr', 'Medtr8g060730' => 'mtr', 'Medtr8g067230' => 'mtr', 'Medtr8g076010' => 'mtr', 'Medtr8g080900' => 'mtr', 'Medtr8g106000' => 'mtr', 'Medtr8g446780' => 'mtr', 'Medtr8g446800' => 'mtr', 'MELO3C023455.2' => 'cme', 'Nitab4.5_0002046g0080' => 'nta', 'Nitab4.5_0005934g0020' => 'nta', 'Nitab4.5_0008673g0010' => 'nta', 'Nn8g39731' => 'nnu', 'Peaxi162Scf00332g00225' => 'pax', 'PGR102G0655' => 'pgr', 'PGSC0003DMG400014130' => 'stu', 'PGSC0003DMG400014131' => 'stu', 'Phvul.010G159100' => 'pvu', 'Phvul.010G159200' => 'pvu', 'Potri.003G179100' => 'ptr', 'Prupe.3G095400' => 'ppe', 'Psat0s1674g0080' => 'psa', 'Psat0s538g0040' => 'psa', 'Psat3g012240' => 'psa', 'Psat3g014520' => 'psa', 'Psat3g051760' => 'psa', 'Psat3g054040' => 'psa', 'Psat3g054120' => 'psa', 'Psat3g054200' => 'psa', 'Psat3g054280' => 'psa', 'Psat3g054360' => 'psa', 'Psat3g055200' => 'psa', 'Psat3g055240' => 'psa', 'Psat3g057080' => 'psa', 'Psat3g131680' => 'psa', 'Psat5g104160' => 'psa', 'Psat7g041280' => 'psa', 'Psat7g112360' => 'psa', 'Psat7g255480' => 'psa', 'Psat7g256280' => 'psa', 'Psat7g258640' => 'psa', 'Psat7g258680' => 'psa', 'Psat7g258720' => 'psa', 'Psat7g261360' => 'psa', 'Psat7g261440' => 'psa', 'Psat7g261480' => 'psa', 'Psat7g261520' => 'psa', 'Psat7g261560' => 'psa', 'Psat7g261600' => 'psa', 'Psat7g261720' => 'psa', 'Psat7g261760' => 'psa', 'Psat7g263440' => 'psa', 'QL05p034226' => 'qlo', 'RcHm_v2.0_Chr2g0133501' => 'rch', 'Rhsim01G0015100' => 'rsi', 'Rhsim01G0015200' => 'rsi', 'Rhsim01G0029300' => 'rsi', 'Rhsim01G0029400' => 'rsi', 'Rhsim01G0029500' => 'rsi', 'Rhsim01G0029600' => 'rsi', 'Rhsim01G0029700' => 'rsi', 'Rhsim01G0029800' => 'rsi', 'Rhsim01G0029900' => 'rsi', 'Rhsim01G0030000' => 'rsi', 'Rhsim01G0030100' => 'rsi', 'Rhsim01G0030200' => 'rsi', 'Rhsim01G0030300' => 'rsi', 'Rhsim01G0030400' => 'rsi', 'Rhsim01G0030500' => 'rsi', 'Rhsim01G0030600' => 'rsi', 'Rhsim01G0030700' => 'rsi', 'Rhsim01G0030800' => 'rsi', 'Rhsim01G0030900' => 'rsi', 'Rhsim01G0031000' => 'rsi', 'Rhsim01G0031100' => 'rsi', 'Rhsim01G0031200' => 'rsi', 'Rhsim01G0031300' => 'rsi', 'Rhsim01G0031400' => 'rsi', 'Rhsim01G0031500' => 'rsi', 'Rhsim01G0031600' => 'rsi', 'Rhsim01G0031700' => 'rsi', 'Rhsim01G0031800' => 'rsi', 'Rhsim01G0031900' => 'rsi', 'Rhsim01G0032000' => 'rsi', 'Rhsim01G0032100' => 'rsi', 'Rhsim01G0032200' => 'rsi', 'Rhsim01G0032300' => 'rsi', 'Rhsim01G0032400' => 'rsi', 'Rhsim01G0032500' => 'rsi', 'Rhsim01G0032600' => 'rsi', 'Rhsim01G0032800' => 'rsi', 'Rhsim01G0032900' => 'rsi', 'Rhsim01G0082800' => 'rsi', 'Rhsim02G0048100' => 'rsi', 'Rhsim02G0048200' => 'rsi', 'Rhsim03G0090200' => 'rsi', 'Rhsim04G0152300' => 'rsi', 'Rhsim05G0166000' => 'rsi', 'Rhsim05G0166100' => 'rsi', 'Rhsim06G0127200' => 'rsi', 'Rhsim06G0127300' => 'rsi', 'Rhsim06G0127500' => 'rsi', 'Rhsim06G0127600' => 'rsi', 'Rhsim06G0134200' => 'rsi', 'Rhsim06G0134500' => 'rsi', 'Rhsim12G0117900' => 'rsi', 'RhsimUnG0035500' => 'rsi', 'RhsimUnG0227200' => 'rsi', 'RhsimUnG0243700' => 'rsi', 'RhsimUnG0244000' => 'rsi', 'RhsimUnG0244100' => 'rsi', 'RhsimUnG0244200' => 'rsi', 'RhsimUnG0244300' => 'rsi', 'RhsimUnG0244400' => 'rsi', 'Sabra03G0131300' => 'sbr', 'Sc10g0006180' => 'sci', 'Sc12g0008560' => 'sci', 'Sc12g0009000' => 'sci', 'Sc25g0001130' => 'sci', 'Sc25g0001140' => 'sci', 'Sed0011616' => 'sed', 'SEGI_04733' => 'sgi', 'Sopen03g036110' => 'spe', 'Sp5g35130' => 'spa', 'TAR636G1678' => 'tar', 'THA.LOC104812449' => 'tha', 'Thecc.06G037000' => 'tca', 'Thecc.06G037100' => 'tca', 'Thecc.06G037400' => 'tca', 'Thhalv10018340m.g' => 'esa', 'TPR.G1111' => 'tpr', 'TPR.G1358' => 'tpr', 'TPR.G15114' => 'tpr', 'TPR.G15115' => 'tpr', 'TPR.G15122' => 'tpr', 'TPR.G15124' => 'tpr', 'TPR.G15128' => 'tpr', 'TPR.G15180' => 'tpr', 'TPR.G15685' => 'tpr', 'TPR.G15687' => 'tpr', 'TPR.G15691' => 'tpr', 'TPR.G15695' => 'tpr', 'TPR.G15706' => 'tpr', 'TPR.G15707' => 'tpr', 'TPR.G15720' => 'tpr', 'TPR.G15724' => 'tpr', 'TPR.G15726' => 'tpr', 'TPR.G16304' => 'tpr', 'TPR.G16396' => 'tpr', 'TPR.G17814' => 'tpr', 'TPR.G18060' => 'tpr', 'TPR.G18387' => 'tpr', 'TPR.G18440' => 'tpr', 'TPR.G18547' => 'tpr', 'TPR.G18559' => 'tpr', 'TPR.G19224' => 'tpr', 'TPR.G21219' => 'tpr', 'TPR.G21482' => 'tpr', 'TPR.G22352' => 'tpr', 'TPR.G22462' => 'tpr', 'TPR.G22597' => 'tpr', 'TPR.G22697' => 'tpr', 'TPR.G23034' => 'tpr', 'TPR.G23081' => 'tpr', 'TPR.G23929' => 'tpr', 'TPR.G25394' => 'tpr', 'TPR.G25741' => 'tpr', 'TPR.G25998' => 'tpr', 'TPR.G26002' => 'tpr', 'TPR.G26004' => 'tpr', 'TPR.G26006' => 'tpr', 'TPR.G26304' => 'tpr', 'TPR.G28774' => 'tpr', 'TPR.G29719' => 'tpr', 'TPR.G29721' => 'tpr', 'TPR.G29724' => 'tpr', 'TPR.G29726' => 'tpr', 'TPR.G29727' => 'tpr', 'TPR.G29730' => 'tpr', 'TPR.G29733' => 'tpr', 'TPR.G29734' => 'tpr', 'TPR.G29908' => 'tpr', 'TPR.G29931' => 'tpr', 'TPR.G31141' => 'tpr', 'TPR.G31991' => 'tpr', 'TPR.G3279' => 'tpr', 'TPR.G35158' => 'tpr', 'TPR.G37434' => 'tpr', 'TPR.G37654' => 'tpr', 'TPR.G38610' => 'tpr', 'TPR.G38710' => 'tpr', 'TPR.G38764' => 'tpr', 'TPR.G38777' => 'tpr', 'TPR.G38795' => 'tpr', 'TPR.G38799' => 'tpr', 'TPR.G38803' => 'tpr', 'TPR.G38812' => 'tpr', 'TPR.G577' => 'tpr', 'TPR.G6402' => 'tpr', 'TPR.G7594' => 'tpr', 'TPR.G8602' => 'tpr', 'TPR.G8603' => 'tpr', 'TPR.G8606' => 'tpr', 'TPR.G8802' => 'tpr', 'TPR.G8970' => 'tpr', 'TPR.G9338' => 'tpr', 'TPR.G9658' => 'tpr', 'TPR.G9668' => 'tpr', 'TPR.G9673' => 'tpr', 'TPR.G9682' => 'tpr', 'TPR.G9688' => 'tpr', 'TPR.G9690' => 'tpr', 'TPR.G9692' => 'tpr', 'TPR.G9694' => 'tpr', 'TPR.G9875' => 'tpr', 'TPR.G9884' => 'tpr', 'TPR.G9967' => 'tpr', 'TWI12G1478' => 'twi', 'TWI75G0494' => 'twi', 'vmacro12363' => 'vma', 'vmacro12364' => 'vma', 'VMungo0331G0565' => 'vmu', 'VMungo0331G0655' => 'vmu' ) $gf_id = 'HOM05D001219' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001219' ) $data_identifier = 'HOM05D001219' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 1, 'aly' => (int) 1, 'arhy' => (int) 19, 'ath' => (int) 1, 'atr' => (int) 1, 'acertr' => (int) 1, 'cqu' => (int) 22, 'bol' => (int) 1, 'bra' => (int) 1, 'can' => (int) 2, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 8, 'cde' => (int) 1, 'cfa' => (int) 1, 'ccl' => (int) 1, 'cil' => (int) 1, 'cla' => (int) 1, 'col' => (int) 17, 'cpa' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 1, 'dzi' => (int) 6, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 5, 'fve' => (int) 2, 'gma' => (int) 3, 'ghi' => (int) 2, 'gra' => (int) 1, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 1, 'lsa' => (int) 1, 'mes' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 151, 'cme' => (int) 1, 'nta' => (int) 3, 'nnu' => (int) 1, 'pax' => (int) 1, 'pgr' => (int) 1, 'stu' => (int) 2, 'pvu' => (int) 2, 'ptr' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 31, 'qlo' => (int) 1, 'rch' => (int) 1, 'rsi' => (int) 60, 'sbr' => (int) 1, 'sci' => (int) 5, 'sed' => (int) 1, 'sgi' => (int) 1, 'spe' => (int) 1, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 1, 'tca' => (int) 3, 'esa' => (int) 1, 'tpr' => (int) 87, 'twi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo0331G0655' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 0